1. Data and associated plots based on the Ct values

1.1 Sample metadata - Data table

Download Sample_metadata.csv

1.2 Ct value - Data table

Download Ct values.csv

1.3 Housekeeping Genes Ct value - Data table

Download Housekeeping Genes Ct values.csv

1.4 Box Plot - Ct values of Housekeeping Genes based on ‘sample plate effect’

1.5 Box Plot - Ct values of all samples based on ‘sample plate effect’

1.6 Density Plot - Ct values of all samples’

1.7 Density Plot - Ct values of all samples based on ‘sample plate effect’ - color fill

1.8 Density Plot - Ct values of all samples’ based on ‘sample plate effect’ - semi-transparent fill

1.9 Scree Plot to determine No. of PCs - Ct values of all samples

1.10 PCA Plot - Ct values of all samples based on ‘sample plate effect + type’

1.11 PCA Plot - Ct values of all samples based on ‘type + timepoints’

1.12 PCA Plot with ellipse - Ct values of all samples based on ‘type + timepoints’

1.13 PCA Plot with ellipse - Ct values of all samples based on ‘timepoints + type’

2. Data and associated plots based on the Negative Delta Ct values [log normalized]

2.1 Delta Ct value - Data table

Download Delta Ct.csv

2.2 Negative Delta Ct value [log normalized] - Data table

Download Negative Delta Ct.csv

2.3 Box Plot - Negative Delta Ct values [log normalized] of all samples based on ‘sample plate effect’

2.4 Density Plot - Negative DCt Values [log normalized] of all samples’

2.5 Density Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect’ - color fill

2.6 Density Plot - Negative Delta Ct Values [log normalized] of all samples’ based on ‘sample plate effect’ - semi-transparent fill

2.7 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] of all samples

2.8 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect + type’

2.9 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’

2.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’

2.11 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘timepoints + type’

2.12 Delta Delta Ct (Covid-19 vs. Healthy Control) - Data table

Download DDCt Covid19 vs Healthy Control.csv

2.13 Fold Change - Linear (Covid-19 vs. Healthy Control) - Data table

Download Fold Change Linear Covid19 vs Healthy Control.csv

2.14 Fold Change - Inverse Scale (Covid-19 vs. Healthy Control) - Data table

Download Fold Change Linear Inverse Covid19 vs Healthy Control.csv

2.15 Fold Change - Log Scale (Covid-19 vs. Healthy Control) - Data table

Download Fold Change Log Covid19 vs Healthy Control.csv

2.16 Delta Delta Ct [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

Download DDCt Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv

2.17 Fold Change - Linear [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

Download Fold Change Linear Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv

2.18 Fold Change - Inverse Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

Download Fold Change Linear Inverse Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv

2.19 Fold Change - Log Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

Download Fold Change Log Covid19 Timepoints (TP 1-4) vs Healthy Control (TP1).csv

2.20 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between Covid-19 vs. Healthy Control - Data table

Download Statistical Analysis Covid19 vs Healthy Control.csv

2.21 Venn Diagram - between Covid-19 vs. Healthy Control - Data table

2.22 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

Download Statistical Analysis [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)].csv

2.23 Venn Diagram from limma - between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

3. Data and associated plots based on the Negative Delta Ct values [log normalized] - Batch Corrected (ComBat function from SVA- R Package)

3.1 Negative Delta Ct value [log normalized] - Batch Corrected - Data table

Download Negative Delta Ct Batch Corrected.csv

3.2 Box Plot - Negative Delta Ct values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’

3.3 Density Plot - Negative DCt Values [log normalized] - Batch Correction of all samples’

3.4 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’ - color fill

3.5 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples’ based on ‘sample plate effect’ - semi-transparent fill

3.6 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] - Batch Correction of all samples

3.7 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of of all samples based on ‘sample plate effect + type’

3.8 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’

3.9 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’

3.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘timepoints + type’

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